NIHU is one of the four inter-university research institute corporations in Japan, along with the National Institutes of Natural Sciences, the Research Organization for Information and Systems and the High Energy Accelerator Research Organization.
The chief executive is the president who is selected by a committee of experts in the humanities and related disciplines. A vice-president and several executive directors are appointed to assist the leadership. Three committees, the Strategic Planning Committee, Administrative Council and Education and Research Council, discuss important matters concerning the operation of the organization. The Advisory Board, consisting of the president, NIHU’s executive directors and the heads of NIHU’s six institutes, discuss matters relating to cooperation between NIHU headquarters and its institutes.
In 2016, two new centers, the Center for Transdisciplinary Innovation (CTI) and the Center for Information and Public Relations (CIP) were established to improve governance at NIHU.